But, in a split decision, the advertising body ruled against the billboards, stating "targeting individual companies is provocative and taking advocacy a step further than is necessary."
Federated Farmers said it believed everyone had the right to express strong views but Feds environment spokesperson Chris Allen said "as the ASA Complaints Board ruling underlines, over-simplification of issues and targeting of two farmer-owned companies is misleading and overly provocative".
All three complainants said the billboards made a false claim and one, Alan Emerson, stated: "The billboards are untrue, gross exaggeration, puffery and deliberate hyperbole that are designed to mislead."
"A majority of farmers are working hard and investing significantly to limit run-off, improve water quality and protect biodiversity," Allen said.
"Federated Farmers takes every opportunity it can to promote sound farm management and environmental stewardship.
"There's more to do but it's not helpful when lobby groups ignore the substantial progress already achieved, vilifies just one section of New Zealand society and fails to acknowledge that our water quality is also hit by urban sewage and stormwater run-off, industrial pollution and the effects of drought.
"I'd like to see Greenpeace work with Federated Farmers and encourage the continued uptake of good farm management practices across the nation.
"In the spirit of co-operation, I'm sure we can organise a group of farmers to help Greenpeace take down the offending billboards."
Greenpeace campaigner Gen Toop has warned upholding the decision could have a "chilling effect" on environmental and social advocacy.
"Civil society must be able to hold individual companies to account, especially when they are responsible for environmental destruction," Toop said.
"It is very disturbing that the ASA has taken a position that companies which pollute the environment are above criticism. Free speech is a vital part of our democratic society."
Greenpeace said, in a statement, the billboards - which were positioned on arterial routes around the country - were the first tactic in it's new campaign to ban synthetic nitrogen fertiliser.
Some of the reasons the ASA gave for its ruling included: "The font for the text "#TooManyCows" was much smaller and harder to read than the main message "Ravensdown and Balance Pollute Rivers", and, as a result, this additional text could easily be missed, thereby distorting the message. And that "the message is over-simplified and potentially unclear".